Parallel modeling of the electric field distribution in the brain

The term "Brain Imaging" identi�es a set of techniques to analyze the structure and/or functional behavior of the brain in normal and/or pathological situations. These techniques are largely used in the study of brain activity. In addition to clinical usage, analysis of brain activity is gaining popularity in others recent �fields, i.e. Brain Computer Interfaces (BCI) and the study of cognitive processes. In this context, usage of classical solutions (e.g. f MRI, PET-CT) could be unfeasible, due to their low temporal resolution, high cost and limited portability. For these reasons alternative low cost techniques are object of research, typically based on simple recording hardware and on intensive data elaboration process. Typical examples are ElectroEncephaloGraphy (EEG) and Electrical Impedance Tomography (EIT), where electric potential at the patient's scalp is recorded by high impedance electrodes. In EEG potentials are directly generated from neuronal activity, while in EIT by the injection of small currents at the scalp. To retrieve meaningful insights on brain activity from measurements, EIT and EEG relies on detailed knowledge of the underlying electrical properties of the body. This is obtained from numerical models of the electric �field distribution therein. The inhomogeneous and anisotropic electric properties of human tissues make accurate modeling and simulation very challenging, leading to a tradeo�ff between physical accuracy and technical feasibility, which currently severely limits the capabilities of these techniques. Moreover elaboration of data recorded requires usage of regularization techniques computationally intensive, which influences the application with heavy temporal constraints (such as BCI). This work focuses on the parallel implementation of a work-flow for EEG and EIT data processing. The resulting software is accelerated using multi-core GPUs, in order to provide solution in reasonable times and address requirements of real-time BCI systems, without over-simplifying the complexity and accuracy of the head models.

Use of shared memory in the context of embedded multi-core processors: exploration of the technology and its limits

Modern embedded systems embrace many-core shared-memory designs. Due to constrained power and area budgets, most of them feature software-managed scratchpad memories instead of data caches to increase the data locality. It is therefore programmers’ responsibility to explicitly manage the memory transfers, and this make programming these platform cumbersome. Moreover, complex modern applications must be adequately parallelized before they can the parallel potential of the platform into actual performance. To support this, programming languages were proposed, which work at a high level of abstraction, and rely on a runtime whose cost hinders performance, especially in embedded systems, where resources and power budget are constrained. This dissertation explores the applicability of the shared-memory paradigm on modern many-core systems, focusing on the ease-of-programming. It focuses on OpenMP, the de-facto standard for shared memory programming. In a first part, the cost of algorithms for synchronization and data partitioning are analyzed, and they are adapted to modern embedded many-cores. Then, the original design of an OpenMP runtime library is presented, which supports complex forms of parallelism such as multi-level and irregular parallelism. In the second part of the thesis, the focus is on heterogeneous systems, where hardware accelerators are coupled to (many-)cores to implement key functional kernels with orders-of-magnitude of speedup and energy efficiency compared to the “pure software” version. However, three main issues rise, namely i) platform design complexity, ii) architectural scalability and iii) programmability. To tackle them, a template for a generic hardware processing unit (HWPU) is proposed, which share the memory banks with cores, and the template for a scalable architecture is shown, which integrates them through the shared-memory system. Then, a full software stack and toolchain are developed to support platform design and to let programmers exploiting the accelerators of the platform. The OpenMP frontend is extended to interact with it.

Proposal of a Continuous Read-out Implementation in the ALICE-TOF detector

The main purpose of ultrarelativistic heavy-ion collisions is the investigation of the QGP. The ALICE experiment situated at the CERN has been specifically designed to study heavy-ion collisions for centre-of-mass energies up to 5.5 per nucleon pair. Extended particle identification capability is one of the main characteristics of the ALICE experiment. In the intermediate momentum region (up to 2.5 GeV/c for pi/K and 4 GeV/c for K/p), charged particles are identified in the ALICE experiment by the Time of Flight (TOF) detector. The ALICE-TOF system is a large-area detector based on the use of Multi-gap Resistive Plate Chamber (MRPC) built with high efficiency, fast response and intrinsic time resolution better than 40 ps. This thesis work, developed with the ALICE-TOF Bologna group, is part of the efforts carried out to adapt the read-out of the detector to the new requirements after the LHC Long Shutdown 2. Tests on the feasibility of a new read-out scheme for the TOF detector have been performed. In fact, the achievement of a continuous read-out also for the TOF detector would not be affordable if one considers the replacement of the TRM cards both for hardware and budget reasons. Actually, the read-out of the TOF is limited at 250 kHz i.e. it would be able to collect up to just a fourth of the maximum collision rate potentially achievable for pp interactions. In this Master’s degree thesis work, I discuss a different read-out system for the ALICE-TOF detector that allows to register all the hits at the interaction rate of 1 MHz foreseen for pp interactions after the 2020, by using the electronics currently available. Such solution would allow the ALICE-TOF detector to collect all the hits generated by pp collisions at 1 MHz interaction rate, which corresponds to an amount four times larger than that initially expected at such frequencies with the triggered read-out system operated at 250 kHz for LHC Run 3. The obtained results confirm that the proposed read-out scheme is a viable option for the ALICE TOF detector. The results also highlighted that it will be advantageous if the ALICE-TOF group also implement an online monitoring system of noisy channels to allow their deactivation in real time.

Thermal right-handed neutrino self-energy in the non-relativistic regime

Recently the issue of radiative corrections to leptogenesis has been raised. Considering the "strong washout" regime, in which OPE-techniques permit to streamline the setup, we report the thermal self-energy matrix of heavy right-handed neutrinos at NLO (resummed 2-loop level) in Standard Model couplings. The renormalized expression describes flavour transitions and "inclusive" decays of chemically decoupled right-handed neutrinos. Although CP-violation is not addressed, the result may find use in existing leptogenesis frameworks.

Distribution of muscarinic receptor subtypes and interstitial cells of Cajal in the gastrointestinal tract of healthy dairy cows

OBJECTIVE: To describe the distribution of muscarinic receptor subtypes M(1) to M(5) and interstitial cells of Cajal (ICCs) in the gastrointestinal tract of healthy dairy cows. SAMPLE POPULATION: Full-thickness samples were collected from the fundus, corpus, and pyloric part of the abomasum and from the duodenum, ileum, cecum, proximal loop of the ascending colon, and both external loops of the spiral colon of 5 healthy dairy cows after slaughter. PROCEDURES: Samples were fixed in paraformaldehyde and embedded in paraffin. Muscarinic receptor subtypes and ICCs were identified by immunohistochemical analysis. RESULTS: Staining for M(1) receptors was found in the submucosal plexus and myenteric plexus. Antibodies against M(2) receptors stained nuclei of smooth muscle cells only. Evidence of M(3) receptors was found in the lamina propria, in intramuscular neuronal terminals, on intermuscular nerve fibers, and on myocytes of microvessels. There was no staining for M(4) receptors. Staining for M(5) receptors was evident in the myocytes of microvessels and in smooth muscle cells. The ICCs were detected in the myenteric plexus and within smooth muscle layers. Distribution among locations of the bovine gastrointestinal tract did not differ for muscarinic receptor subtypes or ICCs. CONCLUSIONS AND CLINICAL RELEVANCE: The broad distribution of M(1), M(3), M(5), and ICCs in the bovine gastrointestinal tract indicated that these components are likely to play an important role in the regulation of gastrointestinal tract motility in healthy dairy cows. Muscarinic receptors and ICCs may be implicated in the pathogenesis of motility disorders, such as abomasal displacement and cecal dilatation-dislocation.

Quantitative mRNA analysis of adrenergic receptor subtypes in the intestines of healthy dairy cows and dairy cows with cecal dilatation-dislocation

OBJECTIVE: To investigate the distribution of mRNA coding for 9 adrenoceptor subtypes in the intestines of healthy dairy cows and cows with cecal dilatationdislocation (CDD). SAMPLE POPULATION: Full-thickness specimens of the intestinal wall were obtained from the ileum, cecum, proximal loop of the ascending colon (PLAC), and external loop of the spiral colon (ELSC) of 15 cows with CDD (group 1) and 15 healthy (control) cows (group 2, specimens collected during laparotomy; group 3, specimens collected after slaughter). PROCEDURES: Concentrations of mRNA for 9 adrenoceptor subtypes (alpha(1A), alpha(1B), alpha(1D), alpha(2AD), alpha(2B), alpha(2C), beta(1), beta(2), and beta(3)) were measured by quantitative real-time reverse transcriptase-PCR assay. Results were expressed relative to mRNA expression of a housekeeping gene. RESULTS: Expression of mRNA for alpha(1B)-, alpha(2AD)-, alpha(2B)-, beta(1)-, and beta(2)-adrenoceptors was significantly lower in cows with CDD than in control cows. In the ileum, these receptors all had lower mRNA expression in cows with CDD than in control cows. The same effect was detected in the ELSC for mRNA for alpha(2AD)-, alpha(2B)-, beta(1)-, and beta(2)-adrenoceptors, and in the cecum and PLAC for alpha(2B)- and beta(2)-adrenoceptors. Groups did not differ significantly for alpha(1A)-adrenoceptors. The mRNA expression for alpha(1D)-, alpha(2C)-, and beta(3)-adrenoceptors was extremely low in all groups. CONCLUSIONS AND CLINICAL RELEVANCE: Differences in expression of mRNA coding for adrenoceptors, most pronounced in the ileum and spiral colon, between cows with CDD and control cows support the hypothesis of an implication of adrenergic mechanisms in the pathogenesis of CDD in dairy cows.

Distribution of mRNA coding for 5-hydroxytryptamine receptor subtypes in the intestines of healthy dairy cows and dairy cows with cecal dilatation-dislocation

OBJECTIVE: To investigate the distribution of mRNA coding for 7 subtypes of 5-hydroxytryptamine receptors (5-HTRs) in the intestines of healthy dairy cows and dairy cows with cecal dilatation-dislocation (CDD). SAMPLE POPULATION: Full-thickness intestinal wall biopsy specimens were obtained from the ileum, cecum, proximal loop of the ascending colon, and external loop of the spiral colon (ELSC) of 15 cows with CDD (group 1) and 15 healthy dairy cows allocated to 2 control groups (specimens collected during routine laparotomy [group 2] or after cows were slaughtered [group 3]). PROCEDURE: Amounts of mRNA coding for 7 subtypes of 5-HTRs (5-HT1A, 5-HT1B, 5-HT1D, 5-HT1F, 5-HT2A, 5-HT2B, and 5-HT4) were measured by quantitative real-time reverse transcriptase-PCR assay. Results were expressed as the percentage of mRNA expression of a housekeeping gene. RESULTS: Expression of mRNA coding for 5-HTR1B, 5-HTR2B, and 5-HTR4 was significantly lower in cows with CDD than in healthy cows. For 5-HTR2B and 5-HTR4, significant differences between cows with CDD and control cows were most pronounced for the ELSC. Expression of mRNA for 5-HTR1D, 5-HTR1F, and 5-HTR2A was extremely low in all groups, and mRNA for 5-HTR1A was not detected. CONCLUSIONS AND CLINICAL RELEVANCE: Relative concentrations of mRNA coding for 5-HTR1B, 5-HT2B, and 5-HTR4 were significantly lower in the intestines of cows with CDD than in the intestines of healthy dairy cows, especially for 5-HT2B and 5-HTR4 in the ELSC. This supports the hypothesis that serotonergic mechanisms, primarily in the spiral colon, are implicated in the pathogenesis of CDD.

Comparative quantitative assessment of GnRH- and LH-receptor mRNA expression in the urinary tract of sexually intact and spayed female dogs

Ovariectomy interrupts the regulatory loop in the hypothalamus-pituitary-gonad axis, leading to a several-fold increase in gonadotropin levels. This rise in hormonal secretion may play a causal role in ovariectomy-related urinary incontinence. The purpose of this study was to examine the effect of ovariectomy in bitches on the expression of GnRH- and LH-receptors in the lower urinary tract, and assess the relationship between receptor expression and plasma gonadotropin concentrations. Plasma gonadotropins were measured in 37 client-owned bitches. Biopsies were harvested from the mid-ventral bladder wall in all dogs, and from nine further locations within the lower urinary tract in 17 of the 37 animals. Messenger RNA of the LH and GnRH receptors was quantified using RT-PCR with the TaqMan Universal PCR Master Mix. Gonadotropins were measured with a canine-specific FSH-immunoradiometric assay and LH-radioimmunoassay. The hierarchical mixed ANOVA model using MINITAB, Mann-Whitney U-test, unpaired means comparison and linear regressions using StatView were applied for statistical analyses. Messenger RNA for both receptors was detected in all biopsy samples. Age was negatively correlated to mRNA expression of the LH and the GnRH receptors. A relationship between the mRNA values and the plasma gonadotropin concentrations was not established. Evaluation of results within each of the biopsy locations revealed greater LH-receptor expression in the proximal second quarter of the urethra in spayed bitches than in intact bitches (P=0.0481). Increased mRNA expression of LH receptors in this location could possibly play a role in the decrease in closing pressure of the urethra following ovariectomy.

Quantitative mRNA analysis of muscarinic acetylcholine receptors in the intestine of dairy cows with spontaneous caecal dilatation-dislocation

Muscarinic receptors mediate acetylcholine-induced muscular contractions. In this study, mRNA levels of muscarinic receptor subtypes 2 and 3 (M(2) and M(3)) in the ileum, caecum, proximal loop of the ascending colon (PLAC) and external loop of the spiral colon (ELSC) were determined by quantitative polymerase chain reaction in seven cows with caecal dilatation-dislocation (CDD) and seven healthy control cows. Levels of M(2) were significantly lower in the caecum, PLAC and ELSC and levels of M(3) were significantly lower in the ileum, caecum, PLAC and ELSC of cows with CDD compared to healthy cows (P<0.05). Down-regulation of M(3) may play a role in the pathogenesis of CDD.

A Column-Generation Approach for a Short-Term Production Planning Problem in Closed-Loop Supply Chains

We present a new model formulation for a multi-product lot-sizing problem with product returns and remanufacturing subject to a capacity constraint. The given external demand of the products has to be satisfied by remanufactured or newly produced goods. The objective is to determine a feasible production plan, which minimizes production, holding, and setup costs. As the LP relaxation of a model formulation based on the well-known CLSP leads to very poor lower bounds, we propose a column-generation approach to determine tighter bounds. The lower bound obtained by column generation can be easily transferred into a feasible solution by a truncated branch-and-bound approach using CPLEX. The results of an extensive numerical study show the high solution quality of the proposed solution approach.

Thermal right-handed neutrino production rate in the relativistic regime

The production rate of right-handed neutrinos from a Standard Model plasma at a temperature above a hundred GeV is evaluated up to NLO in Standard Model couplings. The results apply in the so-called relativistic regime, referring parametrically to a mass M ~ πT, generalizing thereby previous NLO results which only apply in the non-relativistic regime M ≫ πT. The non-relativistic expansion is observed to converge for M ≳ 15T, but the smallness of any loop corrections allows it to be used in practice already for M ≳ 4T. In the latter regime any non-covariant dependence of the differential rate on the spatial momentum is shown to be mild. The loop expansion breaks down in the ultrarelativistic regime M ≪ πT, but after a simple mass resummation it nevertheless extrapolates reasonably well towards a result obtained previously through complete LPM resummation, apparently confirming a strong enhancement of the rate at high temperatures (which facilitates chemical equilibration). When combined with other ingredients the results may help to improve upon the accuracy of leptogenesis computations operating above the electroweak scale.

Spontaneous supersymmetry breaking in the 2d N=1 Wess-Zumino model

We study the phase diagram of the two-dimensional N = 1 Wess-Zumino model using Wilson fermions and the fermion loop formulation. We give a complete non-perturbative determination of the ground state structure in the continuum and infinite volume limit. We also present a determination of the particle spectrum in the supersymmetric phase, in the supersymmetry broken phase and across the supersymmetry breaking phase transition. In the supersymmetry broken phase we observe the emergence of the Goldstino particle.

SUSYFLAVOR v2: A Computational tool for FCNC and CP-violating processes in the MSSM

We present SUSY_FLAVOR version 2 — a Fortran 77 program that calculates low-energy flavor observables in the general R-parity conserving MSSM. For a set of MSSM parameters as input, the code gives predictions for: 1. Electric dipole moments of the leptons and the neutron. 2. Anomalous magnetic moments (i.e. g − 2) of the leptons. 3. Radiative lepton decays (μ → eγ and τ → μγ , eγ ). 4. Rare Kaon decays (K0 L → π0 ¯νν and K+ → π+ ¯νν). 5. Leptonic B decays (Bs,d → l+l−, B → τ ν and B → Dτ ν). 6. Radiative B decays (B → ¯ Xsγ ). 7. ΔF = 2 processes ( ¯ K0–K0, ¯D–D, ¯Bd–Bd and ¯Bs–Bs mixing). Comparing to SUSY_FLAVOR v1, where the matching conditions were calculated strictly at one-loop level, SUSY_FLAVOR v2 performs the resummation of all chirally enhanced corrections, i.e. takes into account the enhanced effects from tan β and/or large trilinear soft mixing terms to all orders in perturbation theory. Also, in SUSY_FLAVOR v2 new routines calculation of B → (D)τ ν, g − 2, radiative lepton decays and Br(l → l′γ ) were added. All calculations are done using exact diagonalization of the sfermion mass matrices. The program can be obtained from http://www.fuw.edu.pl/susy_flavor.

A reduced model clarifies the role of feedback loops and time delays in the Drosophila circadian oscillator.

Although several detailed models of molecular processes essential for circadian oscillations have been developed, their complexity makes intuitive understanding of the oscillation mechanism difficult. The goal of the present study was to reduce a previously developed, detailed model to a minimal representation of the transcriptional regulation essential for circadian rhythmicity in Drosophila. The reduced model contains only two differential equations, each with time delays. A negative feedback loop is included, in which PER protein represses per transcription by binding the dCLOCK transcription factor. A positive feedback loop is also included, in which dCLOCK indirectly enhances its own formation. The model simulated circadian oscillations, light entrainment, and a phase-response curve with qualitative similarities to experiment. Time delays were found to be essential for simulation of circadian oscillations with this model. To examine the robustness of the simplified model to fluctuations in molecule numbers, a stochastic variant was constructed. Robust circadian oscillations and entrainment to light pulses were simulated with fewer than 80 molecules of each gene product present on average. Circadian oscillations persisted when the positive feedback loop was removed. Moreover, elimination of positive feedback did not decrease the robustness of oscillations to stochastic fluctuations or to variations in parameter values. Such reduced models can aid understanding of the oscillation mechanisms in Drosophila and in other organisms in which feedback regulation of transcription may play an important role.

Kuroshio Intrusion and the Circulation in the South China Sea

The Princeton Ocean Model is used to study the circulation in the South China Sea (SCS) and its seasonal transition. Kuroshio enters ( leaves) the SCS through the southern ( northern) portion of the Luzon Strait. The annually averaged net volume flux through the Luzon Strait is similar to2 Sv into the SCS with seasonal reversals. The inflow season is from May to January with the maximum intrusion of Kuroshio water reaching the western SCS during fall in compensation of summertime surface offshore transport associated with coastal upwelling. From February to April the net transport reverses from the SCS to the Pacific. The intruded Kuroshio often forms an anticyclonic current loop west of the Luzon Strait. The current loop separates near the Dongsha Islands with the northward branch continuously feeding the South China Sea Warm Current (SCSWC) near the shelf break and the westward branch becoming the South China Sea Branch of Kuroshio on the slope, which is most apparent in the fall. The SCSWC appears from December to February on the seaward side of the shelf break, flowing eastward against the prevailing wind. Diagnosis shows that the onshore Ekman transport due to northeasterly monsoon generates upwelling when moving upslope, and the particular distributions of the density and sea level associated with the cross shelf motion supports the SCSWC.